add 去除多余绘图

heatmap_script.R

@@ -1,11 +1,8 @@
 # 加载所需的包
-suppressPackageStartupMessages(library(grid))
-suppressPackageStartupMessages(library(ComplexHeatmap))
 suppressPackageStartupMessages(library(circlize))
 suppressPackageStartupMessages(library(RColorBrewer))
+suppressPackageStartupMessages(library(ComplexHeatmap))
 suppressPackageStartupMessages(library(dendextend))
-suppressPackageStartupMessages(library(dendsort))
-suppressPackageStartupMessages(library(gridBase))
 
 # 从命令行获取参数
 args <- commandArgs(trailingOnly = TRUE)
@@ -21,76 +18,47 @@ output_pdf <- args[2]
 
 # 检查输入文件是否存在
 if (!file.exists(input_csv)) {
-  stop("输入文件不存在，请检查路径是否正确。", call. = FALSE)
+  stop("输入文件不存在。请检查文件路径。", call. = FALSE)
 }
 
-# 加载绘图数据
+# 函数加载和预处理数据
-data <- read.table(file = input_csv, header = TRUE, row.names = 1, sep = ',')
+load_and_preprocess_data <- function(file_path) {
+  data <- read.table(file = file_path, header = TRUE, row.names = 1, sep = ',')
+  data_matrix <- as.matrix(data)
+  normalized_data <- t(scale(t(data_matrix)))
+  normalized_data[is.na(normalized_data)] <- 0
+  return(normalized_data)
+}
 
-# 查看数据
+# 加载和预处理数据
-head(data)
+cir1 <- load_and_preprocess_data(input_csv)
 
-# 转化matrix格式矩阵及数据归一化
+# 打印数据维度和头部
-data <- as.matrix(data)
+print(dim(cir1))
-cir1 <- t(scale(t(data)))
+print(head(cir1))
 
-# 处理 NA 值
+# 定义颜色梯度
-cir1[is.na(cir1)] <- 0
-
-# 查看归一化后的数据
-head(cir1)
-
-# 定义热图颜色梯度
 mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
-mycol1 <- colorRamp2(c(-2, 0, 2), c("#003399", "white", "#cccc00"))
 
-# 打开PDF设备
+# 打开PDF设备，设置宽度和高度相等
-pdf(output_pdf, width = 10, height = 8)
+pdf(output_pdf, width = 8, height = 8)
 
-# 默认参数绘制普通热图
+# 设置绘图参数
-Heatmap(cir1, row_names_gp = gpar(fontsize = 6),
-        column_names_gp = gpar(fontsize = 8),
-        col = mycol,
-        name = "legend")
-
-# 计算数据大小范围
-range(cir1)
-
-# 绘制基础环形热图
-circos.heatmap(cir1, col = mycol)
-circos.clear()
-
-# 在circos.heatmap()中添加参数进行环形热图的调整和美化
 circos.par(gap.after = c(30))
-circos.heatmap(cir1, col = mycol,
-               dend.side = "inside",
-               rownames.side = "outside",
-               rownames.col = "black",
-               rownames.cex = 1.2,
-               rownames.font = 1.2,
-               bg.border = "black",
-               cluster = TRUE)
-circos.clear()
 
-# 聚类树的调整和美化
+# 绘制调整后的圆形热图
-circos.par(gap.after = c(30))
+circos.heatmap(cir1, 
-circos.heatmap(cir1, col = mycol, dend.side = "inside",
+                col = mycol, 
-               rownames.side = "outside",
+                dend.side = "inside", 
-               track.height = 0.28,
+                rownames.side = "outside", 
-               rownames.col = "black",
+                rownames.col = "black", 
-               rownames.cex = 1.3,
+                rownames.cex = 1.3, 
-               rownames.font = 1.3,
+                track.height = 0.35,  # 增加轨道高度
-               cluster = TRUE,
+                cluster = TRUE, 
-               dend.track.height = 0.18,
+                dend.track.height = 0.18, 
-               dend.callback = function(dend, m, si) {
+                dend.callback = function(dend, m, si) {
-                 color_branches(dend, k = 15, col = 1:15)
+                  color_branches(dend, k = 15, col = 1:15)
-               })
+                })
-circos.clear()
-
-# 添加图例标签等
-lg <- Legend(title = "Exp", col_fun = mycol,
-             direction = c("vertical"))
-grid.draw(lg)
 
 # 添加列名
 circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
@@ -98,14 +66,19 @@ circos.track(track.index = get.current.track.index(), panel.fun = function(x, y)
     cn <- colnames(cir1)
     n <- length(cn)
     circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"), 
-                1:n + 5,
+                1:n + 2.5, 
                 cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
   }
 }, bg.border = NA)
 
+# 添加图例
+lg <- Legend(title = "Exp", col_fun = mycol, direction = "vertical")
+grid.draw(lg)
+
+# 清除圆形图
 circos.clear()
 
 # 关闭PDF设备
 dev.off()
 
-message("热图已成功保存到: ", output_pdf)
+message("热图已成功保存至: ", output_pdf)